Genomic and epidemiological surveillance of Zika virus in the Amazon region

• Author(s): Giovanetti, Marta ; Faria, Nuno Rodrigues ; Louren?o, Jos? ; Jesus, Jaqueline Goes de ; Xavier, Joilson ; Claro, Ingra Morales ; Kraemer, Moritz U. G ; Fonseca, Vagner ; Dellicour, Simon ; Th?ze, Julien ; Salles, Flavia da Silva ; Graf, Tiago ; Silveira, Paola Paz ; Nascimento, Valdinete Alves do ; Souza, Victor Costa de ; Iani, Felipe Campos de Melo ; Castilho-Martins, Emerson Augusto ; Cruz, Laura Nogueira ; Wallau, Gabriel ; Fabri, Allison ; Levy, Fl?via ; Quick, Joshua ; Azevedo, Vasco de ; Aguiar, Renato Santana ; Oliveira, Tulio de ; Menezes, Camila B?tto de ; Castilho, Marcia da Costa ; Terra, Tirza Matos ; Silva, Marineide Souza da ; Filippis, Ana Maria Bispo de ; Abreu, Andr? Luiz de ; Oliveira, Wanderson Kleber ; Croda, Julio ; Albuquerque, Carlos F. Campelo de ; Nunes, Marcio Roberto Teixeira ; Sabino, Ester Cerdeira ; Loman, Nicholas ; Naveca, Felipe Gomes ; Pybus, Oliver G ; Alcantara, Luiz Carlos
• Date: 2020
• Origin: Oasisbr
• Subject(s): Zika virus / patogenicidade; Zika virus / isolamento & purifica??o; Infec??o por Zika virus / transmiss?o; Infec??o por Zika virus / gen?tica; Surtos de Doen?as; Manaus (AM)
• Document Type: Journal article
• Language: English

Description

OxfordNanoporeTechnologiesfortechnicalsupportandQIAGENforsupport of the ZIBRA-2 (Zika in Brazil Real Time Analyses-Second Round)project with reagents and equipment. This work was supported by Decit/SCTIE/MoH and CNPq (440685/2016-8 and 440856/2016-7); by CAPES(88887.130716/2016-00, 88881.130825/2016-00, and 88887.130823/2016-00); by the European Union (EU) Horizon 2020 Programme through ZIKAlliance(PRES-005-FEX-17-4-2-33); by the Medical Research Council and FAPESPCADDE partnership award (MR/S0195/1); and by the Oxford Martin School.N.R.F. is supported by a Sir Henry Dale Fellowship (204311/Z/16/Z).M.U.G.K. is supported by The Branco Weiss Fellowship - Society in Science,administered by ETH Zurich, and acknowledges funding from a Google FacultyAward and a Training Grant from the National Institute of Child Health and Hu-man Development (T32HD040128). S.D. is supported by Fonds National de laRecherche Scientifique (FNRS; Belgium). The activities of the A.M.B.F. labora-tory were supported by the Faperj under the grant no. E-26/2002.930/2016, bytheInternational Development Research Centre (IDRC)Canadaunderthe grant108411-001) and the EU Horizon 2020 Programme through ZikaPlan andZikAction (grants 734584 and 734857). M.G. is supported by Fundac ?~ao deAmparo a`Pesquisa do Estado do Rio de Janeiro (FAPERJ)

Funda??o Oswaldo Cruz. Instituto Oswaldo Cruz. Laborat?rio de Flaviv?rus. Rio de Janeiro, RJ, Brazil / Universidade Federal de Minas Gerais. Instituto de Ci?ncias Biol?gicas. Laborat?rio de Gen?tica Celular e Molecular. Belo Horizonte, MG, Brazil.

Universidade Federal de Minas Gerais. Instituto de Ci?ncias Biol?gicas. Laborat?rio de Gen?tica Celular e Molecular. Belo Horizonte, MG, Brazil / University of Oxford. Department of Zoology. Oxford, UK.

University of Oxford. Department of Zoology. Oxford, UK.

Funda??o Oswaldo Cruz. Instituto Oswaldo Cruz. Laborat?rio de Flaviv?rus. Rio de Janeiro, RJ, Brazil

Universidade Federal de Minas Gerais. Instituto de Ci?ncias Biol?gicas. Laborat?rio de Gen?tica Celular e Molecular. Belo Horizonte, MG, Brazil.

Universidade de S?o Paulo. Instituto de Medicina Tropical. S?o Paulo, SP, Brazil.

University of Oxford. Department of Zoology. Oxford, UK.

Universidade Federal de Minas Gerais. Instituto de Ci?ncias Biol?gicas. Laborat?rio de Gen?tica Celular e Molecular. Belo Horizonte, MG, Brazil / University of KwaZuluNatal. College of Health Sciences. KwaZulu-Natal Research Innovation and Sequencing Platform. Durban, South Africa.

Universite ?Libre de Bruxelles. Spatial Epidemiology Lab. Bruxelles, Belgium / KU Leuven. Department of Microbiology and Immunology. Rega Institute. Laboratory for Clinical and Epidemiological Virology. Leuven, Belgium.

University of Oxford. Department of Zoology. Oxford, UK.

Universidade de S?o Paulo. Instituto de Medicina Tropical. S?o Paulo, SP, Brazil.

Funda??o Oswaldo Cruz. Instituto Gon?alo Moniz. Salvador, BA, Brazil.

Funda??o Oswaldo Cruz. Instituto Gon?alo Moniz. Salvador, BA, Brazil.

Funda??o Oswaldo Cruz. Instituto Le?nidas e Maria Deane. Laborat?rio de Ecologia de Doen?as Transmiss?veis na Amaz?nia. Manaus, AM, Brazil.

Funda??o Oswaldo Cruz. Instituto Le?nidas e Maria Deane. Laborat?rio de Ecologia de Doen?as Transmiss?veis na Amaz?nia. Manaus, AM, Brazil.

Universidade Federal de Minas Gerais. Instituto de Ci?ncias Biol?gicas. Laborat?rio de Gen?tica Celular e Molecular. Belo Horizonte, MG, Brazil / Funda??o Ezequiel Dias. Laborat?rio Central de Sa?de P?blica. Belo Horizonte, MG, Brazil.

Universidade Federal do Amap?. Faculdade de Medicina. Macap?, AP, Brazil.

Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Coordena??o Geral dos Laborat?rios de Sa?de P?blica. Bras?lia, DF, Brasil.

Funda??o Oswaldo Cruz. Instituto Aggeu Magalh?es. Recife, PE, Brazil.

Funda??o Oswaldo Cruz. Instituto Oswaldo Cruz. Laborat?rio de Flaviv?rus. Rio de Janeiro, RJ, Brazil.

Funda??o Oswaldo Cruz. Instituto Oswaldo Cruz. Laborat?rio de Flaviv?rus. Rio de Janeiro, RJ, Brazil.

Funda??o Oswaldo Cruz. Instituto Oswaldo Cruz. Laborat?rio de Flaviv?rus. Rio de Janeiro, RJ, Brazil

University of Birmingham. Institute of Microbiology and Infection. Birmingham, UK.

University of Birmingham. Institute of Microbiology and Infection. Birmingham, UK.

Universidade Federal de Minas Gerais. Instituto de Ci?ncias Biol?gicas. Laborat?rio de Gen?tica Celular e Molecular. Belo Horizonte, MG, Brazil.

Funda??o Oswaldo Cruz. Instituto Gon?alo Moniz. Salvador, BA, Brazil.

University of Birmingham. Institute of Microbiology and Infection. Birmingham, UK.

University of KwaZuluNatal. College of Health Sciences. KwaZulu-Natal Research Innovation and Sequencing Platform. Durban, South Africa.

Universidade do Estado do Amazonas. Manaus, AM, Brazil.

Funda??o de Medicina Tropical Doutor Heitor Vieira Dourado. Departamento de Virologia. Manaus, AM, Brasil.

Laborat?rio Central de Sa?de P?blica do Amazonas. Manaus, AM, Brazil.

Laborat?rio Central de Sa?de P?blica do Amazonas. Manaus, AM, Brazil.

Funda??o Oswaldo Cruz. Instituto Oswaldo Cruz. Laborat?rio de Flaviv?rus. Rio de Janeiro, RJ, Brazil.

Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Coordena??o Geral dos Laborat?rios de Sa?de P?blica. Bras?lia, DF, Brasil.

Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Bras?lia, DF, Brazil.

Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Departamento de Vigil?ncia de Doen?as Transmiss?veis. Bras?lia, DF, Brasil.

Organiza??o Pan-Americana da Sa?de / Organiza??o Mundial da Sa?de. Bras?lia, DF, Brazil.

Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil

University of Birmingham. Institute of Microbiology and Infection.Birmingham, UK.

Funda??o Oswaldo Cruz. Instituto Le?nidas e Maria Deane. Laborat?rio de Ecologia de Doen?as Transmiss?veis na Amaz?nia. Manaus, AM, Brazil.

Funda??o Oswaldo Cruz. Instituto Oswaldo Cruz. Laborat?rio de Flaviv?rus. Rio de Janeiro, RJ, Brazil / Universidade Federal de Minas Gerais. Instituto de Ci?ncias Biol?gicas. Laborat?rio de Gen?tica Celular e Molecular. Belo Horizonte, MG, Brazil.

Zika virus (ZIKV) has caused an explosive epidemic linked to severe clinical outcomes in the Americas. As of June 2018, 4,929 ZIKV suspected infections and 46 congenital syndrome cases had been reported in Manaus, Amazonas, Brazil. Although Manaus is a key demographic hub in the Amazon region, little is known about the ZIKV epidemic there, in terms of both transmission and viral genetic diversity. Using portable virus genome sequencing, we generated 59 ZIKV genomes in Manaus. Phylogenetic analyses indicated multiple introductions of ZIKV from northeastern Brazil to Manaus. Spatial genomic analysis of virus movement among six areas in Manaus suggested that populous northern neighborhoods acted as sources of virus transmission to other neighborhoods. Our study revealed how the ZIKV epidemic was ignited and maintained within the largest urban metropolis in the Amazon. These results might contribute to improving the public health response to outbreaks in Brazil.